IMPACT News

Publications

  • Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA. Extending CATH: increasing coverage of the protein structure universe and linking structure with function.” Nucleic Acids Res. 2011 Jan;39(Database issue):D420-6. Epub 2010 Nov 19. PMID: 21097779

  • Hunter, S., Apweiler, R., & Jesus-Martin, M. “Design, Implementation and Updating of Knowledge Bases.” In G. Alterovitz & M. Ramoni (Eds.), Knowledge-Based Bioinformatics: From Analysis to Interpretation, 2010. John Wiley & Sons, Ltd. doi: 10.1002/9780470669716.ch4.

  • Jones, P. “Analysing proteomics identifications in the context of functional and structural protein annotation: integrating annotation using PICR, DAS, and BioMart.” in Methods in molecular biology (Clifton, N.J.), 696, 107-21, 2011. doi: 10.1007/978-1-60761-987-1_7.

  • McDowall, J., & Hunter, S. “InterPro protein classification.” in Methods in molecular biology (Clifton, N.J.), 694, 37-47 (2011). doi: 10.1007/978-1-60761-977-2_3.

  • [In press, International Journal of Systems Biology and Biomedical Technologies] Mitchell AL, Selimas I, Attwood TK “MINOTAUR: A Web-based Annotator-Assistant Tool.”

  • [In press, Database] Jones P, Binns D, McMenamin C, McAnulla C, Hunter S "The InterPro BioMart: Federated Query and Web-Service Access to the InterPro Resource"

  • [In press, Nucleic Acids Res] Yeats C, Lees J, Carter P, Sillitoe I, Orengo C “The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.”

  • [Submitted, Database] Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong S, Mulder N, Hunter S “Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation”

  • [Accepted for publication, Nucleic Acids Res] Yeats C, Lees J, Carter P, Sillitoe I,  Orengo C “The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.”

  • [Submitted, Database] Jones P, Binns D, McMenamin C, McAnulla C, Hunter S "The InterPro BioMart: Federated Query and Web-Service Access to the InterPro Resource"

  • Letunic I, Doerks T, Bork, P (2009) “SMART 6: Recent updates and new developments”. Nucleic Acids Res. 37:D229-32. (doi:10.1093/nar/gkn808)

  • Hunter S, et al. (2009) “InterPro: The integrative protein signature database”. Nucleic Acids Res. 37: D211-5. (doi:10.1093/nar/gkn785)

  • Wilson D, Pethica R, et al. (2009) “SUPERFAMILY – Sophisticated comparative genomics, data mining, visualization and phylogeny”. Nucleic Acids Res. 37: D380-6. (doi:10.1093/nar/gkn762)

  • Lees J, Yeats C, Redfern O, Clegg A, Orengo C. (2010) “Gene3D: merging structure and function for a Thousand genomes.” Nucleic Acids Res. 38:D296-300.

  • Yeats C, Redfern OC, Orengo C. (2010) “A fast and automated solution for accurately resolving protein domain architectures.” Bioinformatics. 29. [Epub ahead of print]

  • Pethica, R., Barker, G., Kovacs, T. and Gough, J. (2010) “TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web.” PLoS ONE 5(1):e8934

  • Chothia, C. and Gough, J. (2009) “Genomic and Structural Aspects of Protein Evolution.” Biochem. J. 419(1):15-28.

  • Madera, M., Calums, R., Thiltgen, G. Karplus, K. and Gough, J. (2010) “Improving protein secondary structure prediction using a simple k-mer model.” Bioinformatics doi: 10.1093/bioinformatics/btq020.

  • Chang C, Coggill P, Bateman A, Finn RD, Cymborowski M, Otwinowski Z, Minor W, Volkart L, Joachimiak A. (2009) "The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes." BMC Struct Biol. 9:75.

  • Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. (2010) "The Pfam protein families database." Nucleic Acids Res. 38 (Database issue):D211-22

  • Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. (2010) "Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain." J Mol Biol. 396(1):31-46.

  • Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Söding J. (2009) "Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors." Bioinformatics. 25(2):159-62.

  • Blankenburg H, Finn RD, Prli?? A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M. (2009) "DASMI: exchanging, annotating and assessing molecular interaction data." Bioinformatics. 25(10):1321-8.

 

Other News

June 2010

(tbc)

December 2010

  • The new InterPro website has been released and is available publicly at: http://wwwdev.ebi.ac.uk/interpro/

November 2010

  • A third IMPACT workshop was held at EBI on November 4th and 5th

May 2010:

  • A second IMPACT workshop was held at EBI on May 5th and 6th.
  • The InterProScan 5 software has been released for beta testing to a small number of users

February 2010:

  • The second periodic review of IMPACT took place on 23rd February 2010 at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK.

December 2009:

  • Matches of all member signature databases to UniParc and UniMES proteins are now available via the InterPro BioMart
  • A web service is now available to which users can submit InterProScan results and obtain automatic annotations for their proteins.  Please contact the PROSITE team for more details.

October 2009:

  • The first IMPACT workshop was held this month.  Course materials can be found here
  • PRIAM is now linked from InterPro entries which are enzyme related
  • The IMPACT conosortium databases are continuing to produce new signatures for inclusion into InterPro.  Please look at individual databases' homepage for more details (via the "Partners" link in the menu above)

September 2009:

  • The first IMPACT training workshop will be held on October 7th and 8th at EBI.  An agenda and link to registration can be found here.

July 2009:

  • HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) is included in InterPro as a new member database.

February 2009:

  • The first periodic review of IMPACT is due to take place on 3rd February 2009 at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK.

December 2008:

  • A large-scale user network is being set-up for users of InterPro and its member database resources. If you would like to be involved, please contact Sarah Hunter 
  • New features have been added to the InterPro Web interface.  Users are now able to see both un-integrated and integrated signatures.  They can also download FASTA sequence sets for their own use.  Please read the InterPro User Manual for more information.
  • The PRINTS database processing code has been update in InterProScan so that the number of false positives is significantly reduced.

June 2008:

  • A user survey regarding the InterPro web site and services has been performed and analysed.  This will influence the re-design of the InterPro web site
  • New PROSITE pattern specificity software (known as PatternScan) has been implemented in InterProScan
  • The coverage of the protein sequence database UniProtKB by InterPro signatures has been analysed and will be used to direct future signature development.

March 2008:

  • XML files containing non-positional signature data are now available through the InterPro FTP site here
  • A new E-value cut-off for SUPERFAMILY running through HMMer has been implemented in InterProScan 

 January 2008:

  • The IMPACT project has begun 

 

Press Releases

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